A new finite layer method (FLM) is presented in this paper for transient flow analysis in layered radial two-zone aquifer systems. A radial two-zone system is an aquifer configuration in which a circular aquifer with finite radius is surrounded by a matrix possessing different permeability and storage properties. The aquifers can be pumped from fully or partially penetrating wells of infinitesimal radius. The trial function for drawdown is obtained through the use of piecewise linear correction functions in the present method. The trial function can satisfy the continuity conditions of flow and possess an appropriate continuity of C(0) at the two-zone interface. On the basis of Galerkin's method and the continuity condition of flow, the finite layer formulation is derived. The proposed method can cope with the anisotropy and layered heterogeneity in radial two-zone aquifer systems. Several numerical examples are presented to verify the validity of the present method through comparison with the analytical solution and the numerical results based on the finite difference method, in which a test of three-dimensional (3D) flow to a partially penetrating well in anisotropic two-zone aquifers is included. Furthermore, an additional application in simulating the two-zone flow in aquitard-aquifer systems is presented to demonstrate the applicability of FLM in modeling flow in more complex aquifer systems.